Biologic electrode array with integrated optical detector

ABSTRACT

A biologic electrode array is formed on a semiconductor substrate. A matrix of electrode sites is disposed on the semiconductor substrate. A matrix of optical detectors is disposed beneath the electrode sites in the semiconductor substrate, wherein each electrode site is associated with a corresponding optical detector. The optical detectors are coupled to detection circuitry formed on the semiconductor substrate. The electrode sites may include slitted electrodes, punctuated electrodes, or optically transparent electrodes.

This application is a continuation of U.S. application Ser. No.09/903,110, filed on Jul. 10, 2001, now issued as U.S. Pat. No.6,682,936, which is a continuation of U.S. application Ser. No.09/364,676, filed Jul. 30, 1999, now issued as U.S. Pat. No. 6,258,606,which is a continuation of U.S. application Ser. No. 08/677,305, filedon Jul. 9, 1996, now issued as U.S. Pat. No. 5,965,452, all of which areincorporated by reference as if set forth fully herein.

FIELD OF THE INVENTION

The present invention relates generally to electronic systems forcarrying out and/or monitoring biologic reactions and, moreparticularly, to the design, fabrication and uses of self-addressable,self-assembling microelectronic systems for carrying out and controllingmulti-step and multiplex reactions in microscopic formats.

BACKGROUND OF THE INVENTION

For some time now, substantial attention has been directed to thedesign, implementation and use of array-based electronic systems forcarrying out and/or monitoring biologic reactions.

For example, it has been recognized that electronic biosensors ofvarious types may be used to monitor (or measure) the progress ofcertain biologic reactions, and that arrays of these sensors may befabricated using techniques similar to those utilized in the integratedcircuits field. As shown in FIG. 1, a typical prior art biosensor 1 mayinclude a biospecific immobilization surface 2 having an immobilizedaffinity ligand 3 bound thereto, a transducer 4 capable of sensing theoccurrence of chemical reactions which may occur between the immobilizedligand 3 and a specific analyte, and an amplification and control unit 5for filter-ing, amplifying and translating signals generated by thetransducer 4 into various measurements useful for monitoring theprogress or occurrence of a selected biologic reaction. Biosensors ofthe type described above are discussed in some detail in ProteinImmobilization, Fundamentals & Applications, R. F. Taylor, ed. (1991)(chapter 8); and Immobilized Affinity Ligand Techniques, Hermanson etal. (1992) (chapter 5).

The fabrication of an array of biosensors is disclosed, for example, inU.S. patent application Ser. No. 07/872,582, entitled “Optical andElectrical Methods and Apparatus for Molecule Detection” (published Nov.14, 1993 as International Publication No. WO93/22678, and hereinafterreferred to as “the Hollis et al. application”) The Hollis et al.application is directed primarily to biosensory devices comprising anarray of test sites which may be electronically addressed using aplurality of conductive leads. Various types of biosensors are describedfor use at the test sites, and it is suggested that the test sites maybe formed in a semiconductor wafer using photolithographic processingtechniques. It is further suggested that the test sites may be coupledto associated detection circuitry via transistor switches using row andcolumn addressing techniques employed, for example, in addressingdynamic random access memory (DRAM) or active matrix liquid crystaldisplay (AMLCD) devices.

In addition to the biosensor devices described above, several devicescapable of delivering an electrical stimulus (or signal) to a selectedlocation (or test site) within a solution or elsewhere, have beendeveloped. As shown in FIG. 2, these devices often include a source 6,such as a current, voltage or power source, an electrode 7 coupled tothe current source 6, a permeation layer 8 formed on one surface of theelectrode 7, and a biologic attachment layer 9 formed upon thepermeation layer 8. The permeation layer 8 provides for free transportof small counter-ions between the electrode 7 and a solution (notshown), and the attachment layer 9 provides for coupling of specificbinding entities.

Exemplary systems of the type described above are disclosed in PCTApplication No. PCT/US94/12270, which was published in May 1995, and isentitled “Self-Addressable Self-Assembling Microelectronic Systems andDevices for Molecular Biological Analysis and Diagnostics,” and PCTApplication No. PCT/US95/08570, which was published on Jan. 26, 1996,and is entitled “Self-Addressable Self-Assembling MicroelectronicSystems and Devices for Molecular Biological Application,” (hereinafter“the Heller et al. applications”) both of which are hereby incorporatedby reference. The Heller et al. applications describe electronic deviceswhich may be fabricated using microlithographic or micromachiningtechniques, and preferably include a matrix of addressablemicro-locations on a surface thereof. Further, individualmicro-locations are configured to electronically control and direct thetransport and attachment of specific binding entities (e.g., nucleicacids, anti-bodies, etc.) to itself. Thus, the disclosed devices havethe ability to actively carry out controlled multi-step and multiplexreactions in microscopic formats. Applicable reactions include, forexample, nucleic acid hybridizations, antibody/antigen reactions,clinical diagnostics, and multi-step combinational biopolymer synthesisreactions.

Additional electronic systems for interfacing with various solutionsand/or biologic entities are disclosed in European Patent ApplicationNo. 89-3133379.3, published Apr. 7, 1990 and entitled “ElectrophoreticSystem;” U.S. Pat. No. 5,378,343, issued Jan. 3, 1995 and entitled“Electrode Assembly Including Iridium Based Mercury UltramicroelectrodeArray;” U.S. Pat. No. 5,314,495, issued May 24, 1995 and entitled“Microelectronic Interface;” and U.S. Pat. No. 5,178,161, issued Jan.12, 1993 and entitled “Microelectronic Interface.”

Those skilled in the art will appreciate, however, that conventionalelectronic systems for carrying out and/or monitoring biologic reactions(including the devices described in the above-referenced patents andpatent applications) are often bulky, expensive and, at times, difficultto control. Moreover, those skilled in the art will appreciate that,because conventional biologic systems often utilize “off-chip” circuitryto generate and control the current/voltage signals which are applied toan array of test sites, it is often difficult without the use of specialequipment to precisely control the current/voltage signals generated atparticular test sites. As for those conventional systems which do employ“on-chip” circuitry to generate and control the current/voltage signalswhich are applied to an array of test sites, in certain casessubstantial difficulties have been encountered where it is desired toprovide separate and distinct stimuli to selected electrode sites withina large array. One reason for this is that, when single site stimulusspecificity is desired within conventional biosensor arrays, that needis often satisfied through the provision of independent signal lines foreach electrode site within the array. As a result, conventional biologicsystems are often more cumbersome and expensive than is desirable.

In view of the above-noted limitations of conventional biologic systems,it is submitted that an improved biologic system which utilizes aminimum of “off-chip” circuitry and enables the use of large arrays ofelectrode sites while providing for very precise control of thevoltages/currents delivered at a given electrode site, would be bothuseful and desirable.

SUMMARY OF THE INVENTION

The present invention is directed to the design, implementation and useof improved electronic systems and devices for carrying out and/ormonitoring biologic reactions.

In one innovative aspect, a biologic electrode array in accordance withthe present invention may comprise a matrix of electrode sites, whereineach electrode site comprises an electrode which is coupled to arespective sample-and-hold circuit via an amplifier circuit (or drivingelement). In a preferred form, the electrodes, amplifiers andsample-and-hold circuits are integral and form an array within a singlesemiconductor chip, such that each sample-and-hold circuit may be loadedwith a predefined voltage provided by a single, time-shareddigital-to-analog converter (DAC). Further, all of the sample-and-holdcircuits may be accessed through a multiplexer which may be scannedthrough some or all of the electrode locations. In this embodiment, eachsample-and-hold circuit may comprise a capacitor and a transistorswitching circuit, the transistor switching circuit, when enabled,providing electrical communication between the capacitor and a sourceline formed in the matrix. However, in alternative embodiments, thesample-and-hold circuits may comprise some other type of memory whichmay be addressed and loaded with a signal (or value) indicative of acharacteristic of an electrical stimulus to be applied at an associatedelectrode. Such alternative memories may include electrically erasableprogrammable read only memory (EEPROM) cells used as an analog memory(e.g., as in the non-volatile analog signal storage chips produced byInformation Storage Devices, Inc., of San Jose, Calif.), or other typesof circuits capable of storing control information and producingproportional analog output values.

In another innovative aspect, a biologic electrode array in accordancewith the present invention may comprise a single semiconductor chiphaving formed thereon a memory (for example, a random access memory(RAM)), a digital-to-analog converter (DAC) coupled to the memory, acounter, a row decoder coupled to the counter and to the memory, acolumn decoder coupled to the counter and to the memory, and a matrix ofactive biologic electrode sites coupled to the row decoder and thecolumn decoder. In use, binary values representing voltages to beapplied at the various electrode sites within the array are stored inthe memory using, for example, an external computer. Then, for eachaddress (or a selected number of addresses) within the array a binaryvalue is read out of the memory and provided to the DAC which, in turn,converts the binary value to a voltage to be stored on the “hold”capacitor at a selected address. Once all of the addresses of the array(or the selected number of addresses) have been scanned in this fashion,the process may be repeated using either the same values initiallystored in the memory or new values depending upon whether or not timevariation of the voltages/currents provided at the various electrodesites is desired. Those skilled in the art will appreciate that thescanning process should be repeated often enough such that the decayover time of the stored voltages on the sample-and-hold circuits (due tounavoidable leakage currents) does not result in an unacceptablevoltage/current errors at the electrodes. If non-volatilesample-and-hold circuits are used (i.e., if EEPROM or some equivalenttechnology is utilized), such decays may not be significant, allowingfor arbitrarily slow update rates.

In an alternative embodiment, the memory, counter and DAC may bedisposed on one or more separate chips.

In view of the foregoing, it will be appreciated that a biologic arrayin accordance with the present invention provides for very precisecontrol of the potentials/currents delivered to individual electrodeswithin the array, while minimizing the utilization of “off-chip”circuitry and overall system costs. Further, by using localsample-and-hold circuits (or other local memory circuits) to control thelevel of electrical stimulus applied to particular test sites, arrays inaccordance with the present invention may achieve a level of stimulusspecificity and electrode utilization far superior to that achievedusing most prior art systems.

In another innovative aspect, the present invention provides for thefabrication of an entire active array surface on a thermally-isolatedmembrane containing on-board, controllable heating elements. By cyclingthe temperature of the heating elements, it is possible to perform DNAamplification in situ, for example, by the polymerase chain reaction.

Finally, in still another innovative aspect, the present inventionprovides for the incorporation of optical fluorescence or absorptiondetection circuitry within a biologic electrode array matrix to improvecoupling of emitted photons into the detection electronics. Morespecifically, in accordance with one embodiment of the presentinvention, a biologically active electrode is formed above a suitableoptical detector such as a MOS-photodiode structure within, for example,a CMOS circuit. In such an embodiment, the electrode may be formed froma substance which is at least partially transparent, or the electrodemay be formed in such a fashion that it permits the passage of lightthrough its body to an underlying photodetector.

In another aspect of the invention, a site for use in a biologicelectrode array is formed on an integrated circuit chip and includes anoptical detector coupled to detection circuitry. The optical detectorand the detection circuitry are formed on the integrated circuit chip.An electrode is disposed on the integrated circuit chip above theoptical detector. A coupling layer is disposed over at least a portionof the surface of the electrode and one or more biomolecules are boundto the coupling layer.

In still another aspect of the invention, a biologic electrode arrayincludes a semiconductor substrate, a matrix of electrode sites disposedon the semiconductor substrate, and a matrix of optical detectorsdisposed beneath the electrode sites in the semiconductor substrate,wherein each electrode site is associated with a corresponding opticaldetector, the optical detectors being coupled to detection circuitryformed on the semiconductor substrate.

In view of the foregoing, it is an object of the present invention toprovide an improved biologic electrode array for carrying out andcontrolling multi-step and multiplex reactions in microscopic formats.

It is another object of the present invention to provide an improvedbiologic electrode array which is compact and minimizes the utilizationof off-chip control circuitry, even for large numbers of electrodes.

It is another object of the present invention to provide an improvedbiologic electrode site which includes a sample-and-hold circuit, andwhich may be fabricated using conventional CMOS semiconductorfabrication techniques.

It is still another object of the present invention to provide animproved biologic electrode array which includes heating elements forenhancing the progression of reactions such as DNA amplification insitu.

It is still another object of the present invention to provide animproved biologic array which includes a plurality of optical detectorsformed beneath selected electrode sites.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is an illustration of a prior art passive biologic system.

FIG. 2 is an illustration of a prior art active biologic system.

FIG. 3 is an illustration of a biologic array in accordance with oneform of the present invention.

FIG. 4( a) is an illustration of a biologic electrode site in accordancewith one form of the present invention.

FIG. 4( b) is a circuit diagram showing in more detail one of theswitching circuits and the amplifier circuit of the biologic electrodesite illustrated in FIG. 4( a).

FIG. 4( c) illustrates how those portions of the electrode siteillustrated in FIG. 4( b) might be fabricated using CMOS circuitry.

FIG. 5 is an illustration of a biologic electrode site which includescircuitry for monitoring an electrical characteristic of an electrodelocated at the site.

FIG. 6( a) illustrates the fabrication of a combined thermally isolatedmembrane and biologic electrode array, wherein the biologic electrodearray is etched onto a back side surface of a silicon substrate.

FIG. 6( b) illustrates the attachment of a low-thermal-conductivitychamber to the combined thermally isolated membrane and biologicelectrode array shown in FIG. 6( a).

FIG. 7 illustrates a biologic electrode site including an opticaldetector in accordance with the present invention.

FIG. 8( a) is a top view of a punctuated, partially transparentelectrode in accordance with one form of the present invention.

FIG. 8( b) is a top view of an alternative embodiment of a partiallytransparent electrode in accordance with the present invention.

DETAILED DESCRIPTION OF PREFERRED EMBODIMENTS

Turning now to the drawings, as shown in FIG. 3, a biologic array 10 inaccordance with one preferred form of the present invention may comprisea matrix of active biologic electrode sites 12, a row decoder 14, acolumn decoder 16, a counter 18, a random access memory (RAM) 20 actingas a look-up table, and a digital-to-analog converter (DAC) 22. In apreferred form, each of the above listed elements may be disposed on asingle semiconductor chip, and the entire array 10 may be fabricatedusing conventional CMOS semiconductor fabrication techniques. Further,in the presently preferred form a computer (not shown) may be used toload data, as needed, into the RAM 20 via, for example, a data inputport 21.

Turning now also to FIG. 4( a), each biologic electrode site 24, whichmakes up the matrix of biologic electrodes 12, may comprise asample-and-hold circuit 26, an amplifier 28 and an electrode 30. In onepreferred form, the sample-and-hold circuit 26 may comprise a capacitor32 and two transistor switches 34 and 36. The switches 34 and 36 areconnected in series and, when closed, provide electrical communicationbetween a voltage source line 37 (coupled to the DAC 22) and thecapacitor 32. The switches 34 and 36 are coupled, respectively, to adesignated row select line 38 and column select line 40 formed withinthe matrix 12.

As shown in FIGS. 4( b) and 4(c), each row select line 38 and eachcolumn select line 40 may comprise, for example, a positive control line(+control line) 41 and a negative control line (−control line) 43, andeach switch 34 or 36 may comprise a CMOS transmission gate, i.e., a PMOSFET 45 having a gate region 47 coupled to the negative control line 43and a NMOS FET 49 having a gate region 51 coupled to the positivecontrol line 41. In addition, the amplifier circuit (or driving element)28 may comprise a PMOS current source 53.

In an alternative embodiment, a single switch, such as that describedabove, may be controlled by a two input logic gate (e.g., an AND or NANDgate) with complementary outputs (e.g., a +control line and −controlline), and may be used to selectively connect the capacitor 32 to thevoltage source line 37. In such an embodiment, the logic gate wouldrespond to a coincidence of signals on the row and column select lines38 and 40, respectively. Further, it may be noted that in some instancesa two transistor transmission gate will not be needed, and a single MOStransistor can be used as a switch. In such a case, the logic gate needonly provide a single output to the switch.

The design, fabrication and function of counters, row decoders, columndecoders, digital-to-analog converters, and random access memories arewell known in the art and, thus, the structure and operation of thoseelements are not discussed in detail herein. Rather, a generaldescription of the function of the biologic electrode array 10 isprovided below.

In use, binary values representing voltages to be applied at the variouselectrode sites 24 within the matrix 12 are stored in the RAM 20 (orother suitable memory device) using, for example, an external computer.Then, for each address (or a selected number of addresses) within thematrix 12 a binary value is read out of the RAM 20 and provided to theDAC 22 which, in turn, converts the binary value to a voltage to bestored on the capacitor 32 located at the selected site address. Anoutput amplifier 28 is coupled between the capacitor 32 and theelectrode 30 and provides an amplified stimulus signal to the electrode30. The output amplifier 28 may comprise a voltage amplifier and/orbuffer and may thus amplify the voltage on the capacitor 32 and providean amplified voltage to the electrode 30. Alternatively, the outputamplifier 28 may comprise a current output amplifier (for example, atransconductance amplifier) and provide a current signal to theelectrode 30. Once all of the addresses of the matrix (or the selectednumber of addresses) have been scanned in this fashion, the process maybe repeated using either the same values initially stored in the RAM 20or new values, depending upon whether or not time variation of thevoltages/currents provided at the various electrode sites is desired.Those skilled in the art will appreciate that the scanning processshould be repeated often enough such that the decay over time of thestored voltages on the capacitors 32 (due to unavoidable leakagecurrents) does not result in an unacceptable voltage/current error atthe electrodes 30.

In equivalent and alternative forms, the counter 18, RAM 20, and DAC 22may be placed on or off of the chip comprising the electrophoreticelectrode array, as a matter of design choice, and if desired, someother type of circuit (for example, a simple counter or shift register)may be used to control the sequential loading of the sample-and-holdcircuits 26 located at the respective electrode sites 24.

Turning now also to FIG. 5, for some applications it may be desirable toprovide for monitoring of the condition (or electrical characteristics)of one or more of the electrodes 30 within the matrix 12. In this case,it is assumed that if the electrode is driven with a known current, thevoltage that develops is sensed, or, if the electrode is driven with aknown voltage, the current that flows is sensed. To allow monitoring ofthe condition of a given electrode 30 a voltage sense amplifier 42 maybe coupled to the electrode 30 and to a secondary multiplexing bus oroutput pin (not shown). The voltage sense amplifier 42 provides anindication of the voltage at the electrode 30 relative to an electricalground (not shown) for the entire array or relative to a selectedreference electrode (not shown) on the array. The voltage of thereference electrode may, in some instances, also be the ground used forthe array. It should be noted that the output of the sense amplifiers 42for the electrode sites 24 in the array may also be multiplexed onto acommon sense signal line, and that the signals provided to the commonsense signal line may be de-multiplexed using conventional circuitry,such as a sample-and-hold circuit (not shown) and an analog-to-digitalconverter (not shown). The common sense signal line may be separate fromthe common signal line (i.e., the voltage source line 37), or it may besame line, in which case, it would be time shared, serving for someselected periods of time to provide charging signals to the capacitors32 of the electrode sites 24, and serving for other periods of time as acarrier for sense signals generated at the electrode sites 24.

In the case where the electrodes 30 are driven by voltage amplifiers 28and the current that flows through the electrode 30 is to be sensed, asense resistor (not shown) may be connected between the output of thevoltage amplifier 28 and the electrode 30, and two inputs of adifferential amplifier circuit (not shown) may be connected across thesense resistor. In such an embodiment, the signal generated at theoutput of the differential amplifier will be proportional to the currentflowing through the electrode 30.

As explained to some extent above, while the embodiments illustrated inFIGS. 4( a) and 5 employ two switches 34 and 36 connected in series tocontrol the loading of the capacitor 32 (one switch being controlled byeach of the row and column lines, respectively) those skilled in the artwill appreciate that the switching function may be implemented in any ofa number of ways. For example, it would be considered equivalent toreplace the switches 34 and 36, shown in FIGS. 4( a) and 5, with CMOStransmission gates or a combination of an AND gate and a switch.

Turning again to FIG. 4( c), in a preferred form the biologic array 10may be fabricated using a CMOS or other active circuit process.Moreover, those skilled in the art will appreciate that completelyfabricated CMOS circuitry embodying some or all of the above-describedfunctions may be post-processed to form the complete active biologicelectrode array 10 described above. For example, as illustrated in FIG.6, the biologic electrodes 30 may be disposed atop the underlying CMOScircuitry and then protected with an overlapping passivation layer 44.Further, openings in the passivation layer 44 may be fabricated toexpose the active regions of the biologic electrodes 30 as well as anyrequired peripheral interconnection sites, e.g., bond-pads (not shown).In such an embodiment, the electrodes 30 may be fabricated fromelectrochemically suitable materials, such as gold, iridium or platinum,and may be deposited and patterned using conventional thin-filmdeposition techniques. The passivation layer 44 may comprise, forexample, plasma-deposited silicon nitride and/or silicon carbide, andopenings in the passivation layer 44 may be formed using conventionalmicrofabrication techniques such as plasma etching. Finally, ifbiomolecules are to be bound on or near the surface of the electrodes30, coupling agents and/or intermediate layers (shown in FIG. 7) may beused.

Turning now to FIGS. 6( a) and 6(b), in another preferred form theentire active surface of the biologic array 10 may be formed on athermally-isolated membrane 46 containing one or more on-board,controllable heating elements (not shown). The thermally-isolatedmembrane can be formed using micromachining techniques well-known in theart. For example, the back-side of the completed CMOS waver containingthe biologic array circuitry and electrodes can be coated with asuitable etch mask (e.g., silicon nitride). The silicon nitride ispatterned using standard techniques to form openings where the membraneis to be formed. The membranes are formed by submerging the wafer in anetching solution (e.g., tetramethylammononium hydroxide loaded withdissolved silicon, as described in Klassen, et al., “MicromachinedThermally Isolated Circuits,” Proceedings of the Solid-State Sensor andActuator Workshop, Hilton Head, S.C., Jun. 3–6, 1996, pp. 127–131). Themembrane can thus be temperature cycled to allow DNA amplification insitu. Further, controllable heating of the membrane may be accomplishedthrough the use of an array of resistors or appropriately biased MOSFETS(metal oxide semiconductor field effect transistors) distributedthroughout the membrane area. Thus, if a solution 48 (shown in FIG. 6(b)) overlying the array 10 is provided with DNA and suitable chemicalsto carry out a polymerase chain reaction (PCR) to amplify the DNA,cycling the temperature of the membrane will allow the desiredamplification. If thermal feedback is desired, the temperature of themembrane may be readily determined. For example, the temperaturecoefficient of resistance of the heater resistors or the forward voltageof diodes incorporated into the membrane may be utilized to provide anindication of the solution temperature. Finally, once the DNA containedwithin the solution 48 is amplified, appropriate chemicals may beinjected into the chamber 50 to effect one or more desired analysissteps. Examples of such chemicals are restriction enzymes, fluorescentlabels and intercalcators, etc.

An exemplary micromachined, membrane-based DNA amplification system hasbeen demonstrated by Northrup, et al. (see Northrup et al., “DNAAmplification with a Microfabricated Reaction Chamber,” Proceedings ofTransducers '93, the 7th International Conference on Solid State Sensorsand Actuators, Yokohama, Japan, Jun. 7–10, 1993, pp. 924–926, which isincorporated herein by reference) and, thus, the specific structure andoperation of the membrane-based DNA amplification system is notdiscussed herein in detail. However, it should be noted that theNorthrup et al. system provides merely for thermal cycling, and has noanalysis or biologic electrode control capabilities. Thus, it isbelieved that those skilled in the art will find a biologic array inaccordance with present invention to be highly advantageous, as such anarray allows for in situ DNA amplification and subsequent analysis usinga single device.

Turning now to FIG. 7, for some applications, it may be desirable toincorporate optical fluorescence or transmittance detection circuitrydirectly into the electrode matrix 12 to improve coupling of emitted ortransmitted photons into any provided detection electronics. In the caseof fluorescence detection, the entire array would be illuminated withlight at wavelength(s) known to excite fluorescence in the fluorescentlylabeled biomolecules such as DNA or intercalators between DNA strands.This light would be detected by the optical detection means located ateach site. In the case of transmittance detection, the entire arraywould be illuminated with light at wavelength(s) known to be attenuatedby the presence of the biomolecules of interest (i.e., the light atthose wavelengths is absorbed by the biomolecules) the presence of thebiomolecules of interest at a given electrode site would be detected byan attenuation of the light sensed by the optical detector local to thatsite. This approach can greatly improve the signal-to-noise ratio (SNR)over the use of an imaging camera remote to the biologic-array 10. Inessence, this involves combining a biologically active electrode (withor without active multiplexing circuitry) above a suitable opticaldetector 50 such as a MOS-photodiode or a charge-coupled device (CCD)structure. In such an embodiment, it may be desirable to utilizetransparent electrodes, such as those formed from indium tin oxide(ITO), or it may be desirable to utilize a slitted or punctuatedelectrode structure, such as that shown in FIGS. 8( a) and 8(b). Byproviding orifices 54 (as shown in FIG. 8( a)) or troughs 56 (shown inFIG. 8( b)) through the surface of the electrode 52 it is possible toallow the passage of light through the electrode 52 to the opticaldetector 50. Those skilled in the art will appreciate that byeliminating the need for an external camera and retaining the ability toperform biologically-controlled hybridizations (or other molecularinteractions), the overall cost of a complete analysis system can begreatly reduced.

While the invention of the subject application may take severalalternative and equivalent forms, specific examples thereof have beenshown in the drawings and are herein described in detail. It should beunderstood, however, that the invention is not to be limited to theparticular forms or methods disclosed, but to the contrary, theinvention is to cover all modifications, equivalents, and alternativesfalling within the spirit and scope of the appended claims.

1. A site for use in a biologic electrode array, the biologic electrodearray being formed on an integrated circuit chip, the biologic electrodearray including a coupling layer, comprising: an optical detectorcoupled to detection circuitry, the optical detector and the detectivecircuitry formed on the integrated circuit chip; an electrode disposedon the integrated circuit chip between the optical detector and thecoupling layer, the electrode covering at least a portion of the opticaldetector; the coupling layer disposed over at least a portion of asurface of the electrode; one or more biomolecules bound to the couplinglayer; at least one switch coupled to the electrode; a voltage line thatis selectively connected to the electrode via the switch; a voltagesource coupled to the voltage line; a local addressable memoryassociated with each electrode of the array, the memory controlling thelevel of electrical stimulus applied to the associated electrode; andwherein the electrode is selected from the group consisting of a slittedelectrode, a punctuated electrode, and an optically transparentelectrode.
 2. A site according to claim 1, wherein the electrodecomprises indium tin oxide.
 3. A site according to claim 1, wherein theoptical detector is a photodiode.
 4. A site according to claim 1,wherein the optical detector is a charge-coupled device.
 5. A siteaccording to claim 1, wherein the biomolecules are nucleic acids.
 6. Asite according to claim 1, further comprising a source of light disposedabove the biologic electrode array.
 7. A biologic electrode arraycomprising: a semiconductor substrate; a coupling layer; a matrix ofoptical detectors; a matrix of electrode sites disposed between thecoupling layer and the matrix of optical detectors, the matrix ofoptical detectors disposed beneath and at least partially covered by theelectrode sites in the semiconductor substrate, wherein each electrodesite is associated with a corresponding optical detector, the opticaldetectors coupled to detection circuitry formed on the semiconductorsubstrate; at least one switch coupled to at least one of the electrodesites within the matrix; a voltage line that is selectively connected tothe at least one electrode via the switch; a voltage source coupled tothe voltage line; a local addressable memory associated with eachelectrode of the array, the memory controlling the level of electricalstimulus applied to the associated electrode; and wherein the electrodesite is selected from the group consisting of a slitted electrode, apunctuated electrode, and an optically transparent electrode.
 8. Anarray according to claim 7, further comprising one or more biomoleculesbound to the coupling layer of at least one electrode site.
 9. An arrayaccording to claim 8, wherein the biomolecules are nucleic acids.
 10. Anarray according to claim 7, wherein the electrodes comprise indium tinoxide.
 11. An array according to claim 7, wherein the optical detectorsare photodiodes.
 12. An array according to claim 7, wherein the opticaldetectors are charge-coupled devices.
 13. An array according to claim 7,further comprising a plurality of row and column lines for addressingindividual electrode sites within the matrix.
 14. An array according toclaim 7, wherein at least a portion of the array is formed using CMOSfabrication techniques.